An Introduction to Maximum-Likelihood Methods in Cryo-EM
10.1016/s0076-6879(10)82011-7
Crossref book-chapter
Elsevier
Methods in Enzymology (78)
Bibliography

Sigworth, F. J., Doerschuk, P. C., Carazo, J.-M., & Scheres, S. H. W. (2010). An Introduction to Maximum-Likelihood Methods in Cryo-EM. Cryo-EM, Part B: 3-D Reconstruction, 263–294.

Authors 4
  1. Fred J. Sigworth (first)
  2. Peter C. Doerschuk (additional)
  3. Jose-Maria Carazo (additional)
  4. Sjors H.W. Scheres (additional)
References 48 Referenced 63
  1. 10.1038/nature05994 / Nature / The molecular architecture of cadherins in native epidermal desmosomes by Al-Amoudi (2007)
  2. 10.1016/j.jsb.2009.02.012 / J. Struct. Biol. / Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules by Baxter (2009)
  3. {'year': '2008', 'author': 'Chen', 'key': '10.1016/S0076-6879(10)82011-7_bib0015'} by Chen (2008)
  4. 10.1146/annurev.biochem.78.070507.140543 / Annu. Rev. Biochem. / The advent of near-atomic resolution in single-particle electron microscopy by Cheng (2009)
  5. 10.1111/j.2517-6161.1977.tb01600.x / J. R. Stat. Soc. Ser. B / Maximum-likelihood from incomplete data via the EM algorithm by Dempster (1977)
  6. 10.1109/18.857786 / IEEE Trans. Inf. Theory / Ab initio reconstruction and experimental design for cryo electron microscopy by Doerschuk (2000)
  7. 10.1093/biomet/65.3.457 / Biometrika / Assessing the accuracy of the maximum likelihood estimator: Observed versus expected fisher information by Efron (1978)
  8. 10.1016/0024-3795(81)90139-7 / Linear Algebra Appl. / Iterative algorithms for large partitioned linear systems, with applications to image reconstruction by Eggermont (1981)
  9. {'year': '2006', 'series-title': 'Three-dimensional Electron Microscopy of Macromolecular Assemblies', 'author': 'Frank', 'key': '10.1016/S0076-6879(10)82011-7_bib0045'} / Three-dimensional Electron Microscopy of Macromolecular Assemblies by Frank (2006)
  10. {'key': '10.1016/S0076-6879(10)82011-7_bib0050', 'first-page': '146', 'article-title': 'Exact filters for general geometry three dimensional reconstruction', 'volume': '73', 'author': 'Harauz', 'year': '1986', 'journal-title': 'Optik'} / Optik / Exact filters for general geometry three dimensional reconstruction by Harauz (1986)
  11. 10.1109/42.363108 / IEEE Trans. Med. Imag. / Accelerated image reconstruction using ordered subsets of projection data by Hudson (1994)
  12. 10.1073/pnas.0809587105 / Proc. Natl. Acad. Sci. USA / Structure of ratcheted ribosomes with tRNAs in hybrid states by Julian (2008)
  13. 10.1016/0304-3991(85)90092-0 / Ultramicroscopy / Three-dimensional reconstruction of the shape of human wart virus using spatial correlations by Kam (1985)
  14. 10.1515/zna-1948-8-1105 / Naturforschung / Polyhedral harmonics by Laporte (1948)
  15. {'year': '2009', 'author': 'Lee', 'key': '10.1016/S0076-6879(10)82011-7_bib0075'} by Lee (2009)
  16. 10.1109/TIP.2007.908298 / IEEE Trans. Image Process. / Exact reduced-complexity maximum likelihood reconstruction of multiple 3-D objects from unlabeled unoriented 2-D projections and electron microscopy of viruses by Lee (2007)
  17. 10.1016/j.ultramic.2008.10.014 / Ultramicroscopy / Reciprocal space representations of helical objects and their projection images for helices constructed from motifs without spherical symmetry by Lee (2009)
  18. 10.1016/S0304-3991(97)00127-7 / Ultramicroscopy / 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs) by Marabini (1998)
  19. 10.1109/78.218151 / IEEE Trans. Signal Process. / A simple derivation of the constrained multiple parameter Cramer-Rao bound by Marzetta (1993)
  20. {'key': '10.1016/S0076-6879(10)82011-7_bib0100', 'series-title': 'Biophysical Electron Microscopy: Basic Concepts and Modern Techniques', 'first-page': '145', 'article-title': 'Image analysis of electron micrographs', 'author': 'Moody', 'year': '1990'} / Biophysical Electron Microscopy: Basic Concepts and Modern Techniques / Image analysis of electron micrographs by Moody (1990)
  21. 10.1016/j.jsb.2003.09.007 / J. Struct. Biol. / On the three-dimensional reconstruction of icosahedral particles by Navaza (2003)
  22. {'key': '10.1016/S0076-6879(10)82011-7_bib0110', 'series-title': 'Learning in Graphical Models', 'first-page': '355', 'article-title': 'A view of the EM algorithm that justifies incremental, sparse, and other variants', 'author': 'Neal', 'year': '1998'} / Learning in Graphical Models / A view of the EM algorithm that justifies incremental, sparse, and other variants by Neal (1998)
  23. 10.1006/jsbi.2001.4369 / J. Struct. Biol. / A novel neural network technique for analysis and classification of EM single-particle images by Pascual-Montano (2001)
  24. 10.1016/S1047-8477(02)00008-4 / J. Struct. Biol. / Quantitative self-organizing maps for clustering electron tomograms by Pascual-Montano (2002)
  25. 10.1016/0304-3991(88)90016-2 / Ultramicroscopy / Three-dimensional reconstruction from electron micrographs of disordered specimens. I. method by Provencher (1988)
  26. 10.1016/j.jsb.2009.04.013 / J. Struct. Biol. by Prust (2009)
  27. 10.1137/1026034 / SIAM Rev. / mixture densities, maximum likelihood and the EM algorithm by Redner (1984)
  28. 10.1016/j.jsb.2003.08.001 / J. Struct. Biol. / Corrim-based alignment for improved speed in single-particle image processing by Sander (2003)
  29. 10.1016/j.molcel.2006.08.021 / Mol. Cell / Organization of core spliceosomal components u5 snRNA loop i and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as revealed by electron cryomicroscopy by Sander (2006)
  30. 10.1107/S0907444909012049 / Acta Crystallogr. D / Introducing robustness to maximum-likelihood refinement of electron-microscopy data by Scheres (2009)
  31. 10.1093/bioinformatics/bti1140 / Bioinformatics / Fast maximum-likelihood refinement of electron microscopy images by Scheres (2005)
  32. 10.1016/j.jmb.2005.02.031 / J. Mol. Biol. / Maximum-likelihood multi-reference refinement for electron microscopy images by Scheres (2005)
  33. 10.1038/nmeth992 / Nat. Methods / Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization by Scheres (2007)
  34. 10.1016/j.str.2007.09.003 / Structure / Modeling experimental image formation for likelihood-based classification of electron microscopy data by Scheres (2007)
  35. 10.1016/j.str.2009.10.009 / Structure / Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization by Scheres (2009)
  36. 10.1016/j.jsb.2009.02.007 / J. Struct. Biol. / Maximum likelihood refinement of electron microscopy data with normalization errors by Scheres (2009)
  37. 10.1006/jsbi.1998.4014 / J. Struct. Biol. / A maximum-likelihood approach to single-particle image refinement by Sigworth (1998)
  38. 10.1016/j.jsb.2003.10.025 / J. Struct. Biol. / Classical detection theory and the cryo-EM particle selection problem by Sigworth (2004)
  39. {'key': '10.1016/S0076-6879(10)82011-7_bib0195', 'first-page': '855', 'article-title': 'Fast, adaptive expectation-maximization alignment for cryo-EM', 'volume': '11', 'author': 'Tagare', 'year': '2008', 'journal-title': 'Med. Image Comput. Comput. Assist. Interv.'} / Med. Image Comput. Comput. Assist. Interv. / Fast, adaptive expectation-maximization alignment for cryo-EM by Tagare (2008)
  40. 10.1016/0304-3991(88)90017-4 / Ultramicroscopy / Three-dimensional reconstruction from electron micrographs of disordered specimens. II. implementation and results by Vogel (1988)
  41. 10.1038/320533a0 / Nature / Envelope structure of semliki forest virus reconstructed from cryo-electron micrographs by Vogel (1986)
  42. 10.1006/jsbi.1997.3934 / J. Struct. Biol. / Electron tomography of single ice-embedded macromolecules: Three-dimensional alignment and classification by Walz (1997)
  43. 10.1006/jsbi.2001.4356 / J. Struct. Biol. / An ab initio algorithm for low-resolution 3-D reconstructions from cryoelectron microscopy images by Yin (2001)
  44. 10.1016/j.jsb.2003.09.023 / J. Struct. Biol. / A statistical approach to computer processing of cryo-electron microscope images: Virion classification and 3-D reconstruction by Yin (2003)
  45. 10.4310/CIS.2004.v4.n1.a4 / Commun. Inf. Syst. / Model calculations for joint pattern recognition and signal reconstruction in cryo electron microscopy by Yin (2004)
  46. 10.1016/j.jsb.2007.09.013 / J. Struct. Biol. / A maximum likelihood approach to two-dimensional crystals by Zeng (2007)
  47. 10.1107/S0108767395012888 / Acta Crystallogr. A / Explicit orthonormal fixed bases for spaces of functions that are totally symmetric under the rotational symmetries of a platonic solid by Zheng (1996)
  48. 10.1016/j.jsb.2003.09.033 / J. Struct. Biol. / Automatic particle selection: Results of a comparative study by Zhu (2004)
Dates
Type When
Created 14 years, 10 months ago (Oct. 2, 2010, 4:41 a.m.)
Deposited 5 months, 3 weeks ago (Feb. 25, 2025, 11:51 p.m.)
Indexed 3 weeks, 1 day ago (July 30, 2025, 10:06 a.m.)
Issued 15 years, 7 months ago (Jan. 1, 2010)
Published 15 years, 7 months ago (Jan. 1, 2010)
Published Print 15 years, 7 months ago (Jan. 1, 2010)
Funders 0

None

@inbook{Sigworth_2010, title={An Introduction to Maximum-Likelihood Methods in Cryo-EM}, ISBN={9780123849915}, ISSN={0076-6879}, url={http://dx.doi.org/10.1016/s0076-6879(10)82011-7}, DOI={10.1016/s0076-6879(10)82011-7}, booktitle={Cryo-EM, Part B: 3-D Reconstruction}, publisher={Elsevier}, author={Sigworth, Fred J. and Doerschuk, Peter C. and Carazo, Jose-Maria and Scheres, Sjors H.W.}, year={2010}, pages={263–294} }